"Searching for specific library documentation and implementation code in a codebase" matching MCP servers:

Enables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

Enables researchers to query public ENA and BioSamples genomics data in plain English through any MCP client, including counting records, searching samples, retrieving sample details, and checking metadata quality against project requirements.

An MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.

A production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.

Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.

Connects to NCBI E-utilities for searching, fetching, and linking biological data across Entrez databases.

An MCP server for the gget bioinformatics library that enables AI assistants to perform complex genomics queries, including gene sequence retrieval, BLAST alignments, and protein structure predictions.

A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

An MCP server that enables scRNA-Seq analysis through natural language, providing tools for data preprocessing, clustering, and biological visualization. It supports both predefined function execution and a flexible code mode powered by a Jupyter backend for automated single-cell transcriptomics workflows.

Enables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.

A server providing access to NCBI E-utilities API for searching and retrieving data from databases like PubMed, Protein, and Nucleotide.

A unified MCP server for biomedical research that connects AI systems to resources like Ensembl, EuropePMC, STRING, and more, enabling retrieval of verified domain-specific information.

A self-driving cheminformatics MCP server that dynamically exposes a growing library of RDKit-based molecular analysis tools (fingerprints, descriptors, substructure matching, drug-likeness filters, and more) as MCP tools, with each skill autonomously implemented and tested by an agent loop without human intervention.

Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.

Enables Claude Code to interact with a TACC or SLURM HPC cluster for bioinformatics pipelines, allowing job management, log reading, file browsing, remote script execution, and job submission through natural language.

A Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.

Enables in-chat scientific viewers for molecular structures, sequence alignments, and slide images, plus data tools for searching structures, fetching sequences, aligning them, and drafting NGS analysis plans.

Enables natural language interaction for scRNA-Seq analysis including preprocessing, clustering, and visualization using the CellRank library. It allows users and agents to perform complex genomic data tasks through standard MCP clients and frameworks.